µCT scanning effects on aDNA and a multi-step workflow for archaeological petrous portions

The petrous portion of the temporal bone (often informally referred to as the "petrous bone") is a key element in human evolutionary studies due to its exceptional preservation of biomolecules and morphological information. Intensive and often redundant sampling raises concerns about sustainability and long-term conservation, however. Digital recording of morphology (micro-computed and medical tomography) can preserve what destructive sampling destroys, enabling future analyses, yet there have been concerns regarding its effect on biomolecular preservation. Here, we present a systematic observational assessment of whether micro-computed tomography (µCT)-a widely used tool for digital preservation-affects ancient DNA (aDNA) integrity in archaeological human petrous portions. We analyzed 93 archaeological samples from Argentina, of which 50 were µCT-scanned prior to molecular analysis and 43 were not. We compared six commonly used molecular parameters, including endogenous DNA content, read length, cytosine deamination patterns, and mitochondrial and nuclear contamination estimates. No statistically significant differences were observed between scanned and unscanned samples across these parameters (Mann-Whitney/Wilcoxon tests, p > 0.05). Although mitochondrial contamination estimates were marginally higher in scanned samples (p = 0.051), they largely remain below the widely accepted 5% threshold for genomic analysis. Moreover, this pattern was not observed when considering nuclear contamination. Within the limits of this non-paired design, these results suggest that µCT imaging, under the scanning parameters applied here, does not introduce large or systematic bias derived from disruptions in standard aDNA preservation metrics. Building on these observations and on our collaborative experience with the shared use of archaeological samples across complementary research lines, and given that our results show that µCT imaging under appropriate scanning conditions does not significantly compromise DNA preservation, we propose a sustainable, multi-step workflow that integrates biological profiling, osteobiography, imaging, and compositional pre-screening prior to molecular sampling. This approach aims to maximize the scientific information obtained from skeletal collections while minimizing destructive practices, thereby promoting ethical and sustainable research on irreplaceable anthropological remains, and fostering interdisciplinary collaboration.

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Journal
PLoS ONE
Published
2026-04-13
DOI
https://doi.org/10.1371/journal.pone.0334682
Primary Topic
Forensic and Genetic Research
Type
article
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article

µCT scanning effects on aDNA and a multi-step workflow for archaeological petrous portions

Luis Tissera, Constanza de la Fuente Castro, Anne Le Maître, Nicolás Rascovan et al.
PLoS ONE
Forensic and Genetic Research
article

µCT scanning effects on aDNA and a multi-step workflow for archaeological petrous portions

Luis Tissera, Constanza de la Fuente Castro, Anne Le Maître, Nicolás Rascovan, Camila Tamburrini, Mirsha Quinto Sánchez, Horacio Chiavazza, María Clara López‐Sosa, Ramiro Barberena, Cassandra Rios, M. Solange Grimoldi, Verónica Silva-Pinto, Ana Solari, Juan Manuel Argüelles, Laura T. Buck, Anne-Marie Pessis, Miguel Ángel Contreras-Sieck, Sebastián Pastor, Paula Novellino, Lumila Paula Menéndez, G. Hernández, Pierre Luisi, Vivette García-Deister, Candela Acosta Morano, Hans Groh, Wara Siles, Bernardo Yáñez, Lorena Becerra-Valdivia, Christine Chappard, Ivan Díaz, Sebastian Giannotti, Daniela Mansegosa, Sebastian Pasqualini, Susan C. Kuzminsky, Sergio Monteiro Da Silva, Daniela Guevara
article en

Abstract

The petrous portion of the temporal bone (often informally referred to as the "petrous bone") is a key element in human evolutionary studies due to its exceptional preservation of biomolecules and morphological information. Intensive and often redundant sampling raises concerns about sustainability and long-term conservation, however. Digital recording of morphology (micro-computed and medical tomography) can preserve what destructive sampling destroys, enabling future analyses, yet there have been concerns regarding its effect on biomolecular preservation. Here, we present a systematic observational assessment of whether micro-computed tomography (µCT)-a widely used tool for digital preservation-affects ancient DNA (aDNA) integrity in archaeological human petrous portions. We analyzed 93 archaeological samples from Argentina, of which 50 were µCT-scanned prior to molecular analysis and 43 were not. We compared six commonly used molecular parameters, including endogenous DNA content, read length, cytosine deamination patterns, and mitochondrial and nuclear contamination estimates. No statistically significant differences were observed between scanned and unscanned samples across these parameters (Mann-Whitney/Wilcoxon tests, p > 0.05). Although mitochondrial contamination estimates were marginally higher in scanned samples (p = 0.051), they largely remain below the widely accepted 5% threshold for genomic analysis. Moreover, this pattern was not observed when considering nuclear contamination. Within the limits of this non-paired design, these results suggest that µCT imaging, under the scanning parameters applied here, does not introduce large or systematic bias derived from disruptions in standard aDNA preservation metrics. Building on these observations and on our collaborative experience with the shared use of archaeological samples across complementary research lines, and given that our results show that µCT imaging under appropriate scanning conditions does not significantly compromise DNA preservation, we propose a sustainable, multi-step workflow that integrates biological profiling, osteobiography, imaging, and compositional pre-screening prior to molecular sampling. This approach aims to maximize the scientific information obtained from skeletal collections while minimizing destructive practices, thereby promoting ethical and sustainable research on irreplaceable anthropological remains, and fostering interdisciplinary collaboration.

PLoS ONEVol. 21(4)
Universidad Mayor de San Andrés (BO), Centre National de la Recherche Scientifique (FR), University of Vienna (AT), University of Minnesota (US), University of Bonn (DE), Consejo Nacional de Investigaciones Científicas y Técnicas (AR), Institut Pasteur (FR), Universidad Nacional de Cuyo (AR), Konrad Lorenz Institute for Evolution and Cognition Research (AT), Universidad Nacional de Córdoba (AR), California State University, Channel Islands (US), Université Paris Cité (FR), Universidad de Buenos Aires (AR), Universidade Federal de Pernambuco (BR), Universidad Católica de Temuco (CL), National University of Catamarca (AR), Universidad de Costa Rica (CR), University of Bristol (GB), Sorbonne Université (FR), University of Oxford (GB), Centro Científico Tecnológico - San Juan (AR), Mediterranean Center for Environmental Studies (ES), Fundação Museu do Homem Americano (BR), Universidad Isalud (AR), Laboratoire d’Imagerie Biomédicale (FR), National Museum of Archaeology (BO), Institute of Paleoprimatology Human Paleontology Evolution and Paleoenvironments (FR), National Archaeological Museum of Spain (ES), Centro Científico Tecnológico - Córdoba (AR), Centro Científico Tecnológico Patagónico (AR), National Institute of Anthropology and History (MX), Liverpool John Moores University (GB), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (MX), University of Chile (CL), Universidad Nacional de La Plata (AR), Universidad Nacional Autónoma de México (MX), Universidad Diego Portales (CL)
Wenner-Gren Foundation, Centre National de la Recherche Scientifique, European Research Council
Life in Land
Openalex Percentile: Top 22%
Forensic and Genetic Research
DOIOpen Access PDFOpenAlex
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